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- PDB-2yhn: The IDOL-UBE2D complex mediates sterol-dependent degradation of t... -

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Basic information

Entry
Database: PDB / ID: 2yhn
TitleThe IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor
ComponentsE3 UBIQUITIN-PROTEIN LIGASE MYLIP
KeywordsLIGASE / E2 LIGASE- E3 LIGASE COMPLEX / RING ZINC-FINGER / UBE2D1 / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of low-density lipoprotein particle clearance / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / cytoskeletal protein binding / VLDLR internalisation and degradation / cholesterol homeostasis / protein destabilization / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / positive regulation of protein catabolic process ...regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of low-density lipoprotein particle clearance / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / cytoskeletal protein binding / VLDLR internalisation and degradation / cholesterol homeostasis / protein destabilization / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of neuron projection development / nervous system development / ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / metal ion binding / plasma membrane / cytosol
Similarity search - Function
MYLIP, FERM domain C-lobe / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / Zinc finger, C3HC4 type (RING finger) / FERM/acyl-CoA-binding protein superfamily ...MYLIP, FERM domain C-lobe / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / Zinc finger, C3HC4 type (RING finger) / FERM/acyl-CoA-binding protein superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Zinc finger RING-type profile. / Zinc finger, RING-type / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase MYLIP
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFairall, L. / Goult, B.T. / Millard, C.J. / Tontonoz, P. / Schwabe, J.W.R.
CitationJournal: Genes Dev. / Year: 2011
Title: The Idol-Ube2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor.
Authors: Zhang, L. / Fairall, L. / Goult, B.T. / Calkin, A.C. / Hong, C. / Millard, C.J. / Tontonoz, P. / Schwabe, J.W.R.
History
DepositionMay 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
B: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9846
Polymers17,7232
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-11.5 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.260, 22.770, 87.838
Angle α, β, γ (deg.)90.00, 116.82, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE MYLIP / INDUCIBLE DEGRADER OF THE LDL-RECEPTOR / IDOL / MYOSIN REGULATORY LIGHT CHAIN INTERACTING PROTEIN / MIR


Mass: 8861.413 Da / Num. of mol.: 2 / Fragment: RING, RESIDUES 369-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA
References: UniProt: Q8WY64, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M SODIUM ACETATE PH 7-8, 16-20% MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→39.19 Å / Num. obs: 2928 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 30.95 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 7.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EB5

3eb5


Resolution: 3→35.37 Å / SU ML: 0.45 / σ(F): 0.05 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.297 130 4.4 %
Rwork0.228 --
obs0.232 2928 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.69 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.9771 Å20 Å23.548 Å2
2--2.4133 Å20 Å2
3----1.4361 Å2
Refinement stepCycle: LAST / Resolution: 3→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 4 0 880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019907
X-RAY DIFFRACTIONf_angle_d0.8421244
X-RAY DIFFRACTIONf_dihedral_angle_d13.531290
X-RAY DIFFRACTIONf_chiral_restr0.053151
X-RAY DIFFRACTIONf_plane_restr0.003161
LS refinement shellResolution: 3.0002→35.3703 Å
RfactorNum. reflection% reflection
Rfree0.297 130 -
Rwork0.2284 2798 -
obs--97 %

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